X-Git-Url: http://source.jalview.org/gitweb/?p=jalviewjs.git;a=blobdiff_plain;f=site%2Fj2s%2Fjalview%2Fio%2FPhylipFile.js;h=b4218f72ad4d48d447e11ea2e6d51555e0353e25;hp=d5782bc3e95b35633cfa59b8e29a5b89f05b3153;hb=b9b7a352eee79b7764c3b09c9d19663075061d8c;hpb=7301a2415adab88038b291fc54caeeb3a5a47a44

diff --git a/site/j2s/jalview/io/PhylipFile.js b/site/j2s/jalview/io/PhylipFile.js
index d5782bc..b4218f7 100644
--- a/site/j2s/jalview/io/PhylipFile.js
+++ b/site/j2s/jalview/io/PhylipFile.js
@@ -1,103 +1,103 @@
-Clazz.declarePackage ("jalview.io");
-Clazz.load (["jalview.io.AlignFile"], "jalview.io.PhylipFile", ["java.io.IOException", "java.lang.StringBuffer"], function () {
-c$ = Clazz.declareType (jalview.io, "PhylipFile", jalview.io.AlignFile);
-Clazz.overrideMethod (c$, "parse", 
-function () {
-try {
-var line = this.nextLine ();
-var lineElements = line.trim ().$plit ("\\s+");
-if (lineElements.length < 2) {
-throw  new java.io.IOException ("First line must contain the number of specifies and number of characters");
-}var numberSpecies = Integer.parseInt (lineElements[0]);
-var numberCharacters = Integer.parseInt (lineElements[1]);
-if (numberSpecies <= 0) {
-return;
-}var sequenceElements =  new Array (numberSpecies);
-var sequences =  new Array (numberSpecies);
-for (var i = 0; i < numberSpecies; i++) {
-line = this.nextLine ();
-var potentialName = line.substring (0, 10);
-var tabIndex = potentialName.indexOf ('\t');
-if (tabIndex == -1) {
-sequenceElements[i] = this.parseId (this.validateName (potentialName));
-sequences[i] =  new StringBuffer (this.removeWhitespace (line.substring (10)));
-} else {
-sequenceElements[i] = this.parseId (this.validateName (potentialName.substring (0, tabIndex)));
-sequences[i] =  new StringBuffer (this.removeWhitespace (line.substring (tabIndex)));
-}}
-if ((sequences[0]).length () != numberCharacters) {
-var i = 0;
-for (line = this.nextLine (); line != null; line = this.nextLine ()) {
-if (line.length > 0) {
-sequences[i++].append (this.removeWhitespace (line));
-}if (i == sequences.length) {
-i = 0;
-}}
-}for (var i = 0; i < numberSpecies; i++) {
-if (sequences[i].length () != numberCharacters) {
-throw  new java.io.IOException (sequenceElements[i].getName () + " sequence is incorrect length - should be " + numberCharacters + " but is " + sequences[i].length ());
-}sequenceElements[i].setSequence (sequences[i].toString ());
-this.seqs.add (sequenceElements[i]);
-}
-} catch (e) {
-if (Clazz.exceptionOf (e, java.io.IOException)) {
-System.err.println ("Exception parsing PHYLIP file " + e);
-e.printStackTrace (System.err);
-throw e;
-} else {
-throw e;
-}
-}
-});
-Clazz.defineMethod (c$, "removeWhitespace", 
- function (txt) {
-return txt.replaceAll ("\\s*", "");
-}, "~S");
-Clazz.defineMethod (c$, "validateName", 
- function (name) {
-var invalidCharacters =  Clazz.newCharArray (-1, ['(', ')', '[', ']', ':', ';', ',']);
-for (var c, $c = 0, $$c = invalidCharacters; $c < $$c.length && ((c = $$c[$c]) || true); $c++) {
-if (name.indexOf (c) > -1) {
-throw  new java.io.IOException ("Species name contains illegal character " + c);
-}}
-return name;
-}, "~S");
-Clazz.overrideMethod (c$, "print", 
-function () {
-var sb =  new StringBuffer (Integer.toString (this.seqs.size ()));
-sb.append (" ");
-sb.append ((this.seqs.size () > 0) ? Integer.toString (this.seqs.get (0).getSequence ().length) : "0").append (this.newline);
-var sequential = false;
-var numInterleavedColumns = 60;
-var sequenceLength = 0;
-for (var s, $s = this.seqs.iterator (); $s.hasNext () && ((s = $s.next ()) || true);) {
-var name = s.getName ();
-if (name.length > 10) {
-name = name.substring (0, 10);
-} else {
-name = String.format ("%1$-10s", [s.getName ()]);
-}sb.append (name);
-if (sequential) {
-sb.append (s.getSequence ());
-} else {
-sequenceLength = s.getSequence ().length;
-sb.append (s.getSequence (0, Math.min (numInterleavedColumns, sequenceLength)));
-}sb.append (this.newline);
-}
-if (!sequential && sequenceLength > numInterleavedColumns) {
-var numMatrics = Clazz.doubleToInt (sequenceLength / numInterleavedColumns);
-if ((sequenceLength % numInterleavedColumns) > 0) {
-numMatrics++;
-}for (var i = 1; i < numMatrics; i++) {
-sb.append (this.newline);
-var start = i * numInterleavedColumns;
-for (var s, $s = this.seqs.iterator (); $s.hasNext () && ((s = $s.next ()) || true);) {
-sb.append (s.getSequence (start, Math.min (start + numInterleavedColumns, sequenceLength))).append (this.newline);
-}
-}
-}return sb.toString ();
-});
-Clazz.defineStatics (c$,
-"FILE_EXT", "phy",
-"FILE_DESC", "PHYLIP");
-});
+Clazz.declarePackage ("jalview.io");
+Clazz.load (["jalview.io.AlignFile"], "jalview.io.PhylipFile", ["java.io.IOException", "java.lang.StringBuffer"], function () {
+c$ = Clazz.declareType (jalview.io, "PhylipFile", jalview.io.AlignFile);
+Clazz.overrideMethod (c$, "parse", 
+function () {
+try {
+var line = this.nextLine ();
+var lineElements = line.trim ().$plit ("\\s+");
+if (lineElements.length < 2) {
+throw  new java.io.IOException ("First line must contain the number of specifies and number of characters");
+}var numberSpecies = Integer.parseInt (lineElements[0]);
+var numberCharacters = Integer.parseInt (lineElements[1]);
+if (numberSpecies <= 0) {
+return;
+}var sequenceElements =  new Array (numberSpecies);
+var sequences =  new Array (numberSpecies);
+for (var i = 0; i < numberSpecies; i++) {
+line = this.nextLine ();
+var potentialName = line.substring (0, 10);
+var tabIndex = potentialName.indexOf ('\t');
+if (tabIndex == -1) {
+sequenceElements[i] = this.parseId (this.validateName (potentialName));
+sequences[i] =  new StringBuffer (this.removeWhitespace (line.substring (10)));
+} else {
+sequenceElements[i] = this.parseId (this.validateName (potentialName.substring (0, tabIndex)));
+sequences[i] =  new StringBuffer (this.removeWhitespace (line.substring (tabIndex)));
+}}
+if ((sequences[0]).length () != numberCharacters) {
+var i = 0;
+for (line = this.nextLine (); line != null; line = this.nextLine ()) {
+if (line.length > 0) {
+sequences[i++].append (this.removeWhitespace (line));
+}if (i == sequences.length) {
+i = 0;
+}}
+}for (var i = 0; i < numberSpecies; i++) {
+if (sequences[i].length () != numberCharacters) {
+throw  new java.io.IOException (sequenceElements[i].getName () + " sequence is incorrect length - should be " + numberCharacters + " but is " + sequences[i].length ());
+}sequenceElements[i].setSequence (sequences[i].toString ());
+this.seqs.add (sequenceElements[i]);
+}
+} catch (e) {
+if (Clazz.exceptionOf (e, java.io.IOException)) {
+System.err.println ("Exception parsing PHYLIP file " + e);
+e.printStackTrace (System.err);
+throw e;
+} else {
+throw e;
+}
+}
+});
+Clazz.defineMethod (c$, "removeWhitespace", 
+ function (txt) {
+return txt.replaceAll ("\\s*", "");
+}, "~S");
+Clazz.defineMethod (c$, "validateName", 
+ function (name) {
+var invalidCharacters =  Clazz.newCharArray (-1, ['(', ')', '[', ']', ':', ';', ',']);
+for (var c, $c = 0, $$c = invalidCharacters; $c < $$c.length && ((c = $$c[$c]) || true); $c++) {
+if (name.indexOf (c) > -1) {
+throw  new java.io.IOException ("Species name contains illegal character " + c);
+}}
+return name;
+}, "~S");
+Clazz.overrideMethod (c$, "print", 
+function () {
+var sb =  new StringBuffer (Integer.toString (this.seqs.size ()));
+sb.append (" ");
+sb.append ((this.seqs.size () > 0) ? Integer.toString (this.seqs.get (0).getSequence ().length) : "0").append (this.newline);
+var sequential = false;
+var numInterleavedColumns = 60;
+var sequenceLength = 0;
+for (var s, $s = this.seqs.iterator (); $s.hasNext () && ((s = $s.next ()) || true);) {
+var name = s.getName ();
+if (name.length > 10) {
+name = name.substring (0, 10);
+} else {
+name = String.format ("%1$-10s", [s.getName ()]);
+}sb.append (name);
+if (sequential) {
+sb.append (s.getSequence ());
+} else {
+sequenceLength = s.getSequence ().length;
+sb.append (s.getSequence (0, Math.min (numInterleavedColumns, sequenceLength)));
+}sb.append (this.newline);
+}
+if (!sequential && sequenceLength > numInterleavedColumns) {
+var numMatrics = Clazz.doubleToInt (sequenceLength / numInterleavedColumns);
+if ((sequenceLength % numInterleavedColumns) > 0) {
+numMatrics++;
+}for (var i = 1; i < numMatrics; i++) {
+sb.append (this.newline);
+var start = i * numInterleavedColumns;
+for (var s, $s = this.seqs.iterator (); $s.hasNext () && ((s = $s.next ()) || true);) {
+sb.append (s.getSequence (start, Math.min (start + numInterleavedColumns, sequenceLength))).append (this.newline);
+}
+}
+}return sb.toString ();
+});
+Clazz.defineStatics (c$,
+"FILE_EXT", "phy",
+"FILE_DESC", "PHYLIP");
+});